mandos.search.pubchem.drugbank_interaction_search._DrugbankInteractionSearch.find() - Code Metrics - Inspection of "feat: more searches and doc" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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by Douglas

created 2021-03-24 04:50 UTC

_DrugbankInteractionSearch.find() A

↳ Parent: mandos.search.pubchem.drugbank_interaction_search

Complexity

Conditions

Size

Total Lines	22
Code Lines	21

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	21
nop	2
dl	0
loc	22
rs	9.376
c	0
b	0
f	0

from dataclasses import dataclass

from typing import Sequence, TypeVar

from mandos.model.pubchem_api import PubchemApi

from mandos.search.pubchem import PubchemHit, PubchemSearch


@dataclass(frozen=True, order=True, repr=True)
class _DrugbankInteractionHit(PubchemHit):
    """"""

    gene_symbol: str
    protein_id: str
    target_name: str
    general_function: str
    specific_function: str


@dataclass(frozen=True, order=True, repr=True)

class DrugbankTargetHit(_DrugbankInteractionHit):
    """"""


@dataclass(frozen=True, order=True, repr=True)

class DrugbankGeneralFunctionHit(_DrugbankInteractionHit):
    """"""


T = TypeVar("T", bound=_DrugbankInteractionHit, covariant=True)



class _DrugbankInteractionSearch(PubchemSearch[T]):
    """"""

    @property
    def data_source(self) -> str:

        return "DrugBank"

    @classmethod
    def _attr(cls):
        raise NotImplementedError()

    def find(self, inchikey: str) -> Sequence[T]:

        data = self.api.fetch_data(inchikey)
        return [
            self.__class__.get_h()(
                record_id=dd.record_id,
                origin_inchikey=inchikey,
                matched_inchikey=data.names_and_identifiers.inchikey,
                compound_id=str(data.cid),
                compound_name=data.name,
                predicate=dd.action,
                object_id=dd.protein_id,
                object_name=getattr(dd, self.__class__._attr()),
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
                search_key=self.key,
                search_class=self.search_class,
                data_source=self.data_source,
                gene_symbol=dd.gene_symbol,
                protein_id=dd.protein_id,
                target_name=dd.target_name,
                general_function=dd.general_function,
                specific_function=dd.specific_function,
            )
            for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions
        ]


class DrugbankTargetSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):

    """"""

    @classmethod
    def _attr(cls):
        return "targetname"


class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):

    """"""

    @classmethod
    def _attr(cls):
        return "generalfunction"


__all__ = [
    "DrugbankTargetHit",
    "DrugbankGeneralFunctionHit",
    "DrugbankTargetSearch",
    "DrugbankGeneralFunctionSearch",
]


1			from dataclasses import dataclass
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			from typing import Sequence, TypeVar
3
4			from mandos.model.pubchem_api import PubchemApi
			0 ignored issues – show Unused Code introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Unused PubchemApi imported from mandos.model.pubchem_api Loading history...
5			from mandos.search.pubchem import PubchemHit, PubchemSearch
6
7
8			@dataclass(frozen=True, order=True, repr=True)
9			class _DrugbankInteractionHit(PubchemHit):
10			""""""
11
12			gene_symbol: str
13			protein_id: str
14			target_name: str
15			general_function: str
16			specific_function: str
17
18
19			@dataclass(frozen=True, order=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
20			class DrugbankTargetHit(_DrugbankInteractionHit):
21			""""""
22
23
24			@dataclass(frozen=True, order=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
25			class DrugbankGeneralFunctionHit(_DrugbankInteractionHit):
26			""""""
27
28
29			T = TypeVar("T", bound=_DrugbankInteractionHit, covariant=True)
			0 ignored issues – show Coding Style Naming introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Class name "T" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
30
31
32			class _DrugbankInteractionSearch(PubchemSearch[T]):
33			""""""
34
35			@property
36			def data_source(self) -> str:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
37			return "DrugBank"
38
39			@classmethod
40			def _attr(cls):
41			raise NotImplementedError()
42
43			def find(self, inchikey: str) -> Sequence[T]:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
44			data = self.api.fetch_data(inchikey)
45			return [
46			self.__class__.get_h()(
47			record_id=dd.record_id,
48			origin_inchikey=inchikey,
49			matched_inchikey=data.names_and_identifiers.inchikey,
50			compound_id=str(data.cid),
51			compound_name=data.name,
52			predicate=dd.action,
53			object_id=dd.protein_id,
54			object_name=getattr(dd, self.__class__._attr()),
			0 ignored issues – show Coding Style Best Practice introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report It seems like `_attr` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
55			search_key=self.key,
56			search_class=self.search_class,
57			data_source=self.data_source,
58			gene_symbol=dd.gene_symbol,
59			protein_id=dd.protein_id,
60			target_name=dd.target_name,
61			general_function=dd.general_function,
62			specific_function=dd.specific_function,
63			)
64			for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions
65			]
66
67
68			class DrugbankTargetSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
69			""""""
70
71			@classmethod
72			def _attr(cls):
73			return "targetname"
74
75
76			class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
77			""""""
78
79			@classmethod
80			def _attr(cls):
81			return "generalfunction"
82
83
84			__all__ = [
85			"DrugbankTargetHit",
86			"DrugbankGeneralFunctionHit",
87			"DrugbankTargetSearch",
88			"DrugbankGeneralFunctionSearch",
89			]
90

dmyersturnbull / mandos

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_DrugbankInteractionSearch.find() A

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